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Fix ch_dbsnp channel #39

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merged 11 commits into from
Sep 27, 2019
Merged

Fix ch_dbsnp channel #39

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653f75b
fix typo for bwaIndex in params.genomes[params.genome]
maxulysse Sep 27, 2019
68360dd
fix log for references files
maxulysse Sep 27, 2019
d021e7b
add more logs
maxulysse Sep 27, 2019
80dcd79
add more logs
maxulysse Sep 27, 2019
578064f
fix params.dbsnpIndex
maxulysse Sep 27, 2019
bfd8c3e
trying things
maxulysse Sep 27, 2019
65195d5
add even more logs
maxulysse Sep 27, 2019
963c0d5
move logs
maxulysse Sep 27, 2019
b19d665
remove bwaIndex from smallGRCh37
maxulysse Sep 27, 2019
6fc6d21
fix ch_dbsnp
maxulysse Sep 27, 2019
bf8b5d5
update CHANGELOG
maxulysse Sep 27, 2019
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -125,6 +125,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
- [#31](https://github.com/nf-core/sarek/pull/31) - Fix rcolorbrewer version according to nf-core lint
- [#33](https://github.com/nf-core/sarek/pull/33) - Fix MD Linting
- [#38](https://github.com/nf-core/sarek/pull/38) - Avoid collision in MultiQC
- [#39](https://github.com/nf-core/sarek/pull/39) - Fix `ch_dbsnp` channel

### `Deprecated`

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1 change: 0 additions & 1 deletion conf/genomes.config
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Expand Up @@ -50,7 +50,6 @@ params {
'smallGRCh37' {
acLoci = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
acLociGC = "${params.genomes_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci.gc"
bwaIndex = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta.{amb,ann,bwt,pac,sa}"
dbsnp = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
germlineResource = "${params.genomes_base}/dbsnp_138.b37.small.vcf.gz"
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41 changes: 25 additions & 16 deletions main.nf
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Expand Up @@ -144,7 +144,7 @@ params.fasta = params.genome && !('annotate' in step) ? params.genomes[params.ge
// The rest can be sorted
params.acLoci = params.genome && 'ascat' in tools ? params.genomes[params.genome].acLoci ?: null : null
params.acLociGC = params.genome && 'ascat' in tools ? params.genomes[params.genome].acLociGC ?: null : null
params.bwaIndex = params.genome && params.fasta && 'mapping' in step ? params.genomes[params.genome].bwa ?: null : null
params.bwaIndex = params.genome && params.fasta && 'mapping' in step ? params.genomes[params.genome].bwaIndex ?: null : null
params.chrDir = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].chrDir ?: null : null
params.chrLength = params.genome && 'controlfreec' in tools ? params.genomes[params.genome].chrLength ?: null : null
params.dbsnp = params.genome && ('mapping' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools) ? params.genomes[params.genome].dbsnp ?: null : null
Expand Down Expand Up @@ -238,10 +238,10 @@ ch_fastaFai = params.fastaFai && !('annotate' in step) ? Channel.value(file(para
ch_germlineResource = params.germlineResource && 'mutect2' in tools ? Channel.value(file(params.germlineResource)) : "null"
ch_intervals = params.intervals && !('annotate' in step) ? Channel.value(file(params.intervals)) : "null"

// knownIndels is currently a list of file, so transform it in a channel
// knownIndels is currently a list of file for smallGRCh37, so transform it in a channel
li_knownIndels = []
if (params.knownIndels && ('mapping' in step)) params.knownIndels.each { li_knownIndels.add(file(it)) }
ch_knownIndels = params.knownIndels ? Channel.value(li_knownIndels.collect()) : "null"
ch_knownIndels = params.knownIndels && params.genome == 'smallGRCh37' ? Channel.value(li_knownIndels.collect()) : params.knownIndels ? Channel.value(file(params.knownIndels)) : "null"

ch_snpEff_cache = params.snpEff_cache ? Channel.value(file(params.snpEff_cache)) : "null"
ch_snpeffDb = params.snpeffDb ? Channel.value(params.snpeffDb) : "null"
Expand Down Expand Up @@ -287,18 +287,25 @@ summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName

if (params.acLoci) summary['acLoci'] = params.acLoci
if (params.acLociGC) summary['acLociGC'] = params.acLociGC
if (params.chrDir) summary['chrDir'] = params.chrDir
if (params.chrLength) summary['chrLength'] = params.chrLength
if (params.dbsnp) summary['dbsnp'] = params.dbsnp
if (params.fasta) summary['fasta'] = params.fasta
if (params.germlineResource) summary['germlineResource'] = params.germlineResource
if (params.intervals) summary['intervals'] = params.intervals
if (params.knownIndels) summary['knownIndels'] = params.knownIndels.join(', ')
if (params.snpeffDb) summary['snpeffDb'] = params.snpeffDb
if (params.vepCacheVersion) summary['vepCacheVersion'] = params.vepCacheVersion
summary['genome'] = params.genome

if (params.fasta) summary['fasta'] = params.fasta
if (params.fastaFai) summary['fastaFai'] = params.fastaFai
if (params.dict) summary['dict'] = params.dict
if (params.bwaIndex) summary['bwaIndex'] = params.bwaIndex
if (params.germlineResource) summary['germlineResource'] = params.germlineResource
if (params.germlineResourceIndex) summary['germlineResourceIndex'] = params.germlineResourceIndex
if (params.intervals) summary['intervals'] = params.intervals
if (params.acLoci) summary['acLoci'] = params.acLoci
if (params.acLociGC) summary['acLociGC'] = params.acLociGC
if (params.chrDir) summary['chrDir'] = params.chrDir
if (params.chrLength) summary['chrLength'] = params.chrLength
if (params.dbsnp) summary['dbsnp'] = params.dbsnp
if (params.dbsnpIndex) summary['dbsnpIndex'] = params.dbsnpIndex
if (params.knownIndels) summary['knownIndels'] = params.knownIndels
if (params.knownIndelsIndex) summary['knownIndelsIndex'] = params.knownIndelsIndex
if (params.snpeffDb) summary['snpeffDb'] = params.snpeffDb
if (params.vepCacheVersion) summary['vepCacheVersion'] = params.vepCacheVersion

if (workflow.profile == 'awsbatch') {
summary['AWS Region'] = params.awsregion
Expand Down Expand Up @@ -758,6 +765,8 @@ markDuplicatesReport = markDuplicatesReport.dump(tag:'MD Report')
(bamMD, bamMDToJoin) = duplicateMarkedBams.into(2)
bamBaseRecalibrator = bamMD.combine(intBaseRecalibrator)

bamBaseRecalibrator = bamBaseRecalibrator.dump(tag:'BAM FOR BASERECALIBRATOR')

// STEP 3: CREATING RECALIBRATION TABLES

process BaseRecalibrator {
Expand All @@ -770,8 +779,8 @@ process BaseRecalibrator {
set idPatient, idSample, file(bam), file(bai), file(intervalBed) from bamBaseRecalibrator
file(dbsnp) from ch_dbsnp
file(dbsnpIndex) from ch_dbsnpIndex
file(dict) from ch_dict
file(fasta) from ch_fasta
file(dict) from ch_dict
file(fastaFai) from ch_fastaFai
file(knownIndels) from ch_knownIndels
file(knownIndelsIndex) from ch_knownIndelsIndex
Expand Down